Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1541
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 37048
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.31
Found at i:6403 original size:78 final size:80
Alignment explanation
Indices: 6282--6505 Score: 287
Period size: 78 Copynumber: 2.8 Consensus size: 80
6272 TTGAATGATG
* * * * *
6282 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGAT-CCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGCTAAG-TCCCGAAGGCAT
6345 TTGTGCGAGATACT-AA
64 TTGTGCGAGATACTAAA
* * *
6361 TTCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTT
*
6425 GTGCGAGTTACTAAA
66 GTGCGAGATACTAAA
* *
6440 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA-CCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AATCCGGGCTAAGTCCCGAAGGCATT
6504 TG
65 TG
6506 AACGAGGAGC
Statistics
Matches: 126, Mismatches: 14, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
77 1 0.01
78 48 0.38
79 27 0.21
80 48 0.38
81 2 0.02
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTT
GTGCGAGATACTAAA
Found at i:6429 original size:40 final size:40
Alignment explanation
Indices: 6282--6505 Score: 287
Period size: 40 Copynumber: 5.7 Consensus size: 40
6272 TTGAATGATG
* * * *
6282 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* *
6322 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACT-AA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
6361 TTCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
6400 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
6440 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
6481 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
6506 AACGAGGAGC
Statistics
Matches: 163, Mismatches: 15, Indels: 12
0.86 0.08 0.06
Matches are distributed among these distances:
38 22 0.13
39 21 0.13
40 110 0.67
41 10 0.06
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:8204 original size:27 final size:27
Alignment explanation
Indices: 8174--8247 Score: 89
Period size: 27 Copynumber: 2.7 Consensus size: 27
8164 AGTCTGACGA
* *
8174 GACATTAAATACAGGATAGTTTGA-TGG
1 GACATTAAACACAGGATAGTAT-ATTGG
8201 GACATTAAACAC-GAGATAGTATATTGG
1 GACATTAAACACAG-GATAGTATATTGG
*
8228 GATATTAAACACAGGATAGT
1 GACATTAAACACAGGATAGT
8248 CGACCGGGAC
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
26 2 0.05
27 38 0.93
28 1 0.02
ACGTcount: A:0.41, C:0.09, G:0.23, T:0.27
Consensus pattern (27 bp):
GACATTAAACACAGGATAGTATATTGG
Found at i:23395 original size:18 final size:17
Alignment explanation
Indices: 23372--23406 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
23362 GATGGGCCGA
*
23372 AATGGGCTATGTGGGCCC
1 AATGGGCT-TGTAGGCCC
23390 AATGGGCTTGTAGGCCC
1 AATGGGCTTGTAGGCCC
23407 CACACGTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.17, C:0.23, G:0.37, T:0.23
Consensus pattern (17 bp):
AATGGGCTTGTAGGCCC
Found at i:23705 original size:27 final size:27
Alignment explanation
Indices: 23652--23705 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
23642 ATGACCAAAA
* * *
23652 TACCCTTATAGGGTAAAATGACTATTT
1 TACCCCTAGAGGGTAAAATGACGATTT
23679 TACCCCTAGAGGGT-AAATGACAGATTT
1 TACCCCTAGAGGGTAAAATGAC-GATTT
23706 GTGCTACGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 7 0.30
27 16 0.70
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (27 bp):
TACCCCTAGAGGGTAAAATGACGATTT
Found at i:23881 original size:26 final size:26
Alignment explanation
Indices: 23830--23881 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
23820 TTTGCCACAT
* **
23830 ATACTGATACTGGTAGCTTTGTTGCG
1 ATACTGATACTGGCAGCTTTACTGCG
*
23856 ATACTGTTACTGGCAGCTTTACTGCG
1 ATACTGATACTGGCAGCTTTACTGCG
23882 CTATTGGTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.37
Consensus pattern (26 bp):
ATACTGATACTGGCAGCTTTACTGCG
Found at i:26102 original size:18 final size:18
Alignment explanation
Indices: 26062--26102 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
26052 AGGCCATCTC
26062 TGGGCTATGTGGGCCACA
1 TGGGCTATGTGGGCCACA
*
26080 CGGGC-ATGTGGGCCCACA
1 TGGGCTATGTGGG-CCACA
26098 TGGGC
1 TGGGC
26103 CCGCAATATC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.15, C:0.27, G:0.41, T:0.17
Consensus pattern (18 bp):
TGGGCTATGTGGGCCACA
Found at i:26684 original size:205 final size:205
Alignment explanation
Indices: 26323--26730 Score: 690
Period size: 205 Copynumber: 2.0 Consensus size: 205
26313 ATACCCGTAT
* *
26323 TGTGACAGCCCAAAATTGACCCTAGTCGGGGAGTGGTTTCGGGACCGCTAAACCGAGTCACCGAA
1 TGTGACAGCCCAAAATTGACCCTAGTCGGGAAGTAGTTTCGGGACCGCTAAACCGAGTCACCGAA
**
26388 AGGTTTGAATGTGATGTTTATTGTCTAGAATATGTAATCATGAATGTGTGAAAATTTCAAGCTTC
66 AGGTTTGAATGTGATACTTATTGTCTAGAATATGTAATCATGAATGTGTGAAAATTTCAAGCTTC
* * *
26453 GATTTAGTCGATTGCATGTGAATTTAGTCAATAGGACTTATATGAGAAAATTTTAAAATGTGATA
131 AATTTAGTCGATTGCATGTAAATTTAGTCAATAGGACTTATATGAGAAAATTCTAAAATGTGATA
26518 GGTCAATGCA
196 GGTCAATGCA
*
26528 TGTGACAGCCCAAAGTTGACCCTAGTCGGGAAGTAGTTTCGGGACCGCTAAACCGAGTCACCGAA
1 TGTGACAGCCCAAAATTGACCCTAGTCGGGAAGTAGTTTCGGGACCGCTAAACCGAGTCACCGAA
* *
26593 ATGTTTGAATGTGATACTTATTGTCTAGAATATGTAATTATGAATGTGTGAAAATTTCAAGCTTC
66 AGGTTTGAATGTGATACTTATTGTCTAGAATATGTAATCATGAATGTGTGAAAATTTCAAGCTTC
* * * *
26658 AATTTGGTTGATTTCATGTAAATTTAGTCAATAGGACTTATGTGAGAAAATTCTAAAATGTGATA
131 AATTTAGTCGATTGCATGTAAATTTAGTCAATAGGACTTATATGAGAAAATTCTAAAATGTGATA
26723 GGTCAATG
196 GGTCAATG
26731 TGTGAGAACC
Statistics
Matches: 189, Mismatches: 14, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
205 189 1.00
ACGTcount: A:0.32, C:0.13, G:0.23, T:0.32
Consensus pattern (205 bp):
TGTGACAGCCCAAAATTGACCCTAGTCGGGAAGTAGTTTCGGGACCGCTAAACCGAGTCACCGAA
AGGTTTGAATGTGATACTTATTGTCTAGAATATGTAATCATGAATGTGTGAAAATTTCAAGCTTC
AATTTAGTCGATTGCATGTAAATTTAGTCAATAGGACTTATATGAGAAAATTCTAAAATGTGATA
GGTCAATGCA
Found at i:28197 original size:80 final size:80
Alignment explanation
Indices: 28113--28357 Score: 221
Period size: 80 Copynumber: 3.1 Consensus size: 80
28103 GGACTAAGAT
* * *
28113 CCGAAGGCATTTGTGCGGGATA-CAAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACT
1 CCGAAGGCATTTGTGCGAGATATCAAA-TCCGGGTTAAGCCCCGAAGGCATTCGTGCGAGATACT
28177 AAATCCGGGTTAAATC
65 AAATCCGGGTTAAATC
* * * * * **
28193 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTA
1 CCGAAGGCATTTGTGCGAGATATCAAATCCGGGTTAAGCCCCGAAGGCATTCGTGCGAGATACTA
**
28258 AATCCGGGTTATGTC
66 AATCCGGGTTAAATC
* * * * * * * ** *
28273 CCGAAGGCA-TTGTGTGAGTTA-CTAAAACCGGGCTATGTCCCGAAGGCATTTGAACGAGGA-GC
1 CCGAAGGCATTTGTGCGAGATATC-AAATCCGGGTTAAGCCCCGAAGGCATTCGTGCGA-GATAC
*
28335 TATATCC-GGTTAAATC
64 TAAATCCGGGTTAAATC
28351 CCGAAGG
1 CCGAAGG
28358 TACGTGATTT
Statistics
Matches: 136, Mismatches: 26, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
78 14 0.10
79 45 0.33
80 74 0.54
81 3 0.02
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (80 bp):
CCGAAGGCATTTGTGCGAGATATCAAATCCGGGTTAAGCCCCGAAGGCATTCGTGCGAGATACTA
AATCCGGGTTAAATC
Found at i:28304 original size:39 final size:40
Alignment explanation
Indices: 28060--28322 Score: 255
Period size: 40 Copynumber: 6.6 Consensus size: 40
28050 TTGAATGCTG
* * * * * *
28060 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTACTAAA
** * * *
28100 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGGGATAC-AAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAA
* * * *
28139 TTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
1 -TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
* *
28180 TCCGGGTTAAATCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
**
28220 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
* *
28260 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
* * *
28299 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
28323 TGAACGAGGA
Statistics
Matches: 192, Mismatches: 26, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
39 36 0.19
40 145 0.76
41 11 0.06
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
Found at i:28342 original size:79 final size:80
Alignment explanation
Indices: 28175--28357 Score: 226
Period size: 79 Copynumber: 2.3 Consensus size: 80
28165 GTGCGAGATA
* * *
28175 CTAAATCCGGGTTAAATCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGG
1 CTAAATCCGGGTTAAATCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
** **
28240 CATTCGTGCGAGTTG
66 CATTCGAACGAGGAG
* ** * *
28255 TTAAATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGG
1 CTAAATCCGGGTTAAATCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
*
28319 CATTTGAACGAGGAG
66 CATTCGAACGAGGAG
*
28334 CTATATCC-GGTTAAATCCCGAAGG
1 CTAAATCCGGGTTAAATCCCGAAGG
28358 TACGTGATTT
Statistics
Matches: 86, Mismatches: 17, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
78 14 0.16
79 46 0.53
80 26 0.30
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (80 bp):
CTAAATCCGGGTTAAATCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
CATTCGAACGAGGAG
Found at i:31352 original size:27 final size:27
Alignment explanation
Indices: 31321--31498 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
31311 TAAATTGTAC
31321 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
31348 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
31374 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
31402 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
31430 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
31457 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
31484 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
31499 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:31435 original size:82 final size:81
Alignment explanation
Indices: 31322--31477 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
31312 AAATTGTACA
* *
31322 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
31386 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
31403 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
31468 TGCGAGTTGA
65 TGCGAATTGA
31478 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:31489 original size:82 final size:81
Alignment explanation
Indices: 31318--31498 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
31308 GATTAAATTG
* *
31318 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
31383 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
31399 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
31463 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
31481 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
31499 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Done.